Reaction kinetics database SABIO-RK

Transcription

1 Reaction kinetics database SABIO-RK Andreas Weidemann HITS Heidelberg, Germany SDBV group COMBINE 15. October 2015

2 SDBV HITS Data management for scientists in life sciences Current major projects: - SABIO-RK: reaction kinetics database - SEEK: for sharing heterogeneous scientific research datasets, including models, data sheets, images... - OperationExplorer: visualization of health data from German hospitals; in collaboration with investigative journalists - Standards: NormSys (Martin) -...

3 Motivation for a reaction kinetics database - quantitative data on reaction kinetics are required e.g. for modellers - problem: hard to find in literature => 2005 / 2006 start of collecting reaction kinetics data, storage in a public accessible database

4 Motivation for a reaction kinetics database - quantitative data on reaction kinetics are required e.g. for modellers - problem: hard to find in literature => 2005 / 2006 start of collecting reaction kinetics data, storage in a public accessible database - SABIO-RK is now part of 'The German Network for Bioinformatics Infrastructure' (de.nbi) which is still in consolidation phase:

5 SABIO-RK: data workflow

6 Data extraction from literature - kinetics data from literature are manually entered via a web form => standardization - the data are manually annotated, e.g. EC number and UniProtKB ID are added - further automatic annotations performed: KEGG, PubChem,... - in agreement Pedro: many data are found in figures / figure legends and tables => not searchable in PubMed abstracts

7 Stored data I

8 Stored data II

9 Data annotation example 'ATP' as compound

10 Public search interface provides many options for detailed search

11 Search results search for 'ATP' and 'homo sapiens'

12 Statistics I as of October 2015: single entries

13 Statistics II kinetic parameter as of October 2015:

14 Data upload and data import into SABIO-RK - direct submission of experimental data - kinetics data in SBML format: upload of SBML file parsing & mapping of entities annotation storage in database

15 RESTfull webservices I - allows programmatic access of data - example: get the list of SABIO kinetic law entries: iclaws/entryids?q=tissue: spleen AND Organism:"Homo sapiens" - returns SBML document

16 RESTfull webservices II application and tools using SABIO-RK webservices: - CellDesigner - JWS Online (Jacky Snoep) - Virtual Cell (VCell, Ion Moraru) - CySabioRK-Plugin for Cytoscape (Matthias König) - BioUML (Mandrik, Kiselev,...) - Path2Models - Bio2RDF - Virtual Liver Network (Matthias König) - University of Manchester (integrated into Taverna workflows) - Systems Biology Metabolic Modeling Assistant SBMM (Univ. Malaga) - SBMLsqueezer (Andreas Dräger) -.

17 Data export - spreadsheets (tables, PDF) - BioPax (main entities, mapping coded by Oliver Ruebenacker) - SBML:

18 Data export in SBML format problems - issues encountered eg: - concentration ranges as boundary conditions - enzyme - compounds - experimental conditions (ph, temp.,...) only in SABIO_RK namespace exported - description of enzyme complexes

19 Data import from SBML files challenges - most of the information in SBML is optional (e.g. units, names) - global and local attributes (e.g. global parameters for whole model and local parameters for single reactions) - sometimes missing organism (e.g. cellular organisms in 74 curated models in BioModels DB) - frequently missing annotations to UniprotKB for enzymes/catalysts (only EC number) - missing parameter definitions (Km, Vmax etc.) - abbreviations for compound names (used only within the model no standard controlled vocabulary)

20 Your data... if you are interested - we could focus on your specific research topic and insert relevant publications - please feel free to send us your data as SMBL - talk to us about uploading and storage of your data in other formats

21 HITS SDBV Group de.nbi